The 44 cent per share loss was better than many on Wall Street had expected. Analysts surveyed by First Call had expected a loss of 61 cents per share in the quarter.
In a statement, the company also said it would not return to profitability in the fourth quarter. Shares of Apple rose one-half to 16-7/16 on Wednesday. The company released its results following the close of trading.
Last week, the company announced the resignation of Gil Amelio as chief executive. At the time, some analysts interpreted the move as a signal that Apple finished the quarter with a worse than expected loss.
Apple said its operating loss in the third quarter narrowed to $60 million from $116 million a year ago.
The company also reported progress in other areas. Apple's gross margins in the quarter rose to 20 per cent, compared to 18.9 percent in the March quarter.
Apple's chief financial officer, Fred Anderson said the company was continuing with its restructuring plans "as evidenced by the significant sequential decrease in operating expenses."
"As anticipated, we experienced sequential revenue growth, largely on the strength of our high-end Macintosh products and robust education market sales."
"Our financial goals are to continue to reduce operating expenses and to return the company to profitability."